cmdahler's post is wonderful, but it isn't really an argument for PDF as an ebook format, but .tex... if the .tex compiling is done by the reader itself, it obviously doesn't matter whether it does it to PDF or to DVI or to some future unknown format so long as it can do so quickly and displays the same.
LaTeX of course is evolving, with LaTeX 3 under development... branches like XeLaTeX are probably already more suitable for ebook readers. Probably what we'd want is a suitably tweaked new branch.
...or, what's almost the same, a tweaked version of HTML or XHTML that has the same power, along with a rendering algorithm that properly obeys good rules of typography, but can adapt those rules somewhat to the preferences of the reader (font size, and so on).
"Tagged PDF" is also a promising new direction, but I think the kinds of tags involved would have to expand dramatically... before long you'd be back to a purely semantic mark-up language.
We shouldn't have to give up kerning, font choice, ligatures, properly displayed and spaced mathematics, and all the other things professional typesetting provides but currently impossible with anything but a PDF on our ebook readers. And this should come from a open source format that it is easily to understand and manipulate (which makes .tex far preferable, IMHO to things like MathML, which looks like a nightmare to manually edit).
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ADE already does fairly decent widow/orphan control. It won't allow single lines of a paragraph to stand alone at the end of a page or at the beginning of a page. The result of this is that you may end up with 2 blank lines at the end of a page (since the bumped paragraph would consist of 3 lines). Something they could do is modulate the leading a tiny bit to spread everything out to make those 2 missing lines less noticeable.
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I wouldn't call that "decent". It's too restrictive. TeX has a "badness" score that can be manually set to various levels for various undesirable features. It'll normally avoid a widow or orphan, but if avoiding badness there creates enough badness elsewhere, it will do an orphan or widow instead of creating that badness. Sometimes, it's very ugly to prevent widows and, especially, orphans, when the space becomes to great. TeX also does "feathering" to space out pages to make them the same height... most of the time. Again, there's a badness score associated with not doing so, and if doing so creates more badness elsewhere it won't.
And the document can customize its own badness weights if it wants to, or leave them at their defaults depending on its particular style and demands.